A genetic discovery related to King Richard III threatens to shake the foundations of the Tudor dynasty and even raises a question mark over the current Queen's royal heritage.

Scientists are now 99.999% sure that the skeleton with a twisted spine found in a Leicester car park in 2012 is that of the last Plantagenet king.

DNA analysis has identified two female-line relatives of the king living today, but new findings show evidence of at least one break in the male line - an historic illegitimacy - which could have far-reaching consequences.

The skeleton's male Y chromosome, only passed from father to son, did not match that of five living individuals who claim a paternal link with King Richard via their shared ancestor, Henry Somerset, the 5th Duke of Beaufort.

A relatively recent break has no royal significance. In contrast, an illegitimacy dating back several centuries to the first Duke of Lancaster, John of Gaunt, or his son John Beaufort, Earl of Somerset, would cast doubt on the succession of a whole series of monarchs including all of the Tudors.

By extension, it could also have implications for the Queen, whose ancestry can be traced back to the founder of the Tudor dynasty, King Henry VII, via James I and Mary, Queen of Scots.

But historian Professor Kevin Schurer, who co-led the research team, insisted: "We are not in any way indicating that Her Majesty should not be on the throne."

John of Gaunt had two sons, John Beaufort and the first Lancastrian king Henry IV, whose direct descendants were Henry V and Henry VI. The Tudor line stems from John Beaufort who was Henry VII's great grandfather.

Richard III was connected to these lineages through his great grandfather Edmund, Duke of York - John of Gaunt's brother.

Prof Schurer, pro-vice chancellor of the University of Leicester, said: "We don't know where the break is, but if there's one particular link that has more significance than any other, it has to be the link between Edward III and his son John of Gaunt.

"J ohn of Gaunt was the father of Henry IV, so if John of Gaunt was not actually the child of Edward III, arguably Henry IV had no legitimate right to the throne, and therefore neither did Henry V, Henry VI, and, indirectly, the Tudors."

Writing in the journal Nature Communications, the scientists said the claim to the crown of the "entire Tudor dynasty" partly rested on its members' descent from John of Gaunt.

They added: "The claim of the Tudor dynasty would also be brought into question if the false paternity occurred between John of Gaunt and his son, John Beaufort, Earl of Somerset."

Richard III was killed at the Battle of Bosworth in 1485, the last significant clash between the forces of the Houses of Lancaster and York in the War of the Roses.

According to historical records he was buried in Grey Friars Church, Leicester, which once stood on the site of the car park where his bones were found.

Examination of the skeleton showed that it had a twisted spine rather than the hunchback for which Richard III was famous. Although he would have walked with one shoulder higher than the other, his deformity could easily have been concealed beneath clothing and armour.

The genetic analysis showed a 96% probability that Richard had blue eyes and a 77% likelihood that he was blond, at least in childhood. It was possible that his hair colour may have darkened with age, said the scientists.

His appearance was probably similar to that depicted in an early portrait held by the Society of Antiquaries in London.

In their paper, the researchers compared the investigation to a missing person case that becomes more difficult over time - in this case, 527 years.

Geneticist Dr Turi King, from the University of Leicester, said: "What we have concluded is that there is, at its most conservative, a 99.999% probability that these are indeed the remains of Richard III. The evidence is overwhelming.

Prof Schurer stressed that the history of the British monarchy took "all kinds of twists and turns" and the Y chromosome discovery had no bearing on the present Queen's right to rule.

He pointed out that the Tudors took the crown essentially "by force" while using the blood line leading to John of Gaunt to back up their claim.

Asked at a press briefing if casting doubt on the Tudors could be said to put into question the legitimacy of subsequent monarchs, he replied: "Some may wish to do that. I don't think I should do it, based on speculation."

Simon Chaplin, director of culture and society at the Wellcome Trust, which co-funded the research, said: "Adding this information to a wealth of existing material about Richard III further highlights the ways in which studying human remains can inform our understanding of the past, and we look forward to learning more about Richard for many years to come."